Generally, there are two separate actions which occur when a tax return is filed. The first action is the filing of the actual tax return, the second action concerns how the subsequent liability or refund is paid (liability) or received (refund) by the taxpayer.
An extension extends the requirement to submit a tax return (by 6 months, typically), but it does not extend the requirement to pay the tax liability. In other words, if an extension is filed and the tax return is submitted after the original filing date (March 15th for S-Corp & Partnership returns, April 15th for personal returns), then the liability that is determined after-the-fact is still due on the original filing date. This is accomplished by estimating your tax liability on the original filing date and paying an estimated tax liability based on that amount on or before the original filing date. If there is no liability determined, then there is no estimated liability payment needed when an extension is filed.